Neisseria gonorrhoeae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253100 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1425761.fastq.gz | Fastqsanger.gz | |||
| SRR1425762.fastq.gz | Fastqsanger.gz | |||
| SRR1425763.fastq.gz | Fastqsanger.gz | |||
| SRR1425764.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs.
2014-09-13 | GSE58650 | GEO
Project description:We report for the first time movement of Correia Repeat Enclosed Elements, through inversion of the element at its chromosomal location. Analysis of Ion Torrent generated genome sequence data from Neisseria gonorrhoeae strain NCCP11945 passaged for 8 weeks in the laboratory under standard conditions and stress conditions revealed a total of 37 inversions: 24 were exclusively seen in the stressed sample; 7 in the control sample; and the remaining 3 were seen in both samples. These inversions have the capability to alter gene expression in N. gonorrhoeae through the previously determined activities of the sequence features of these elements. In addition, the locations of predicted non-coding RNAs were investigated to identify potential associations with CREE. Associations varied between strains, as did the number of each element identified. The analysis indicates a role for CREE in disrupting ancestral regulatory networks, including non-coding RNAs. RNA-Seq was used to examine expression changes related to Correia repeats in the strain
2014-09-13 | E-GEOD-58650 | biostudies-arrayexpress
Project description:We assessed the small RNA transcriptome of Neisseria gonorrhoeae strain MS11 in two genetic backgrounds; using wild type cells as well as cells carrying a rppH insertional mutation. It was found that the presence of the RppH enzyme affected both the quantity and length of small RNAs in various chromosomal locations. However, in comparing the two transcriptomes, we found that not all small RNAs were differentially expressed, suggesting that RppH targets only a subset of transcripts.
2014-11-04 | GSE62926 | GEO
Project description:Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant and a complemented derivative were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, mRNA half-lives increased for 12 genes in Fe-depleted growth conditions, compared to FA1090. Biological functions for the 12 genes controlled by NrrF included energy metabolism, oxidative stress, antibiotic resistance, amino acid synthesis and a regulatory protein whose functions are not fully understood, in addition to hypothetical proteins.
2013-09-27 | GSE48526 | GEO
Project description:We assessed the small RNA transcriptome of Neisseria gonorrhoeae strain MS11 in two genetic backgrounds; using wild type cells as well as cells carrying a rppH insertional mutation. It was found that the presence of the RppH enzyme affected both the quantity and length of small RNAs in various chromosomal locations. However, in comparing the two transcriptomes, we found that not all small RNAs were differentially expressed, suggesting that RppH targets only a subset of transcripts. Analysis of the small RNA transcriptome of N. gonorrhoeae in a wild type and M-NM-^TrppH mutant background.
2014-11-04 | E-GEOD-62926 | biostudies-arrayexpress
Project description:The overall goals and objectives of this study are to investigate the transcriptomics of Neisseria gonorrhoeae using RNA-seq. This work will look at gene expression, start points of transcription, transcriptional termination, and differences between these in different conditions and between strains and growing cultures over time.
2016-05-24 | GSE73032 | GEO
Project description:Deep sequencing of cDNA from Neisseria gonorrhoeae bacteria and human neutrophils, alone and after coincubation.
2018-12-07 | GSE123434 | GEO
Project description:Microarray comparative genome hybridization (mCGH) data was collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae, and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491, and FAM18 and N. gonorrhoeae FA1090.
2007-04-04 | E-TIGR-129 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was the identification of target genes of the Neisseria gonorrhoeae sRNAs NgncR_237, NgncR_162 and NgncR_163. Methods: RNA was isolated from N. gonorrhoeae using the miRNeasy Micro Kit (Qiagen). Enrichment of mRNA was done using the Universal Ribodepletion Kit followed by Next Ultra Directional Library Preparation Kit for Illumina (NEB). The cDNA was sequenced on Illumina HiSeq 3000 platform with 100 bp paired end reads. Adapters from Fastq sequences were removed using cutadapt version 1.2.1. Only reads exceeding a mean base quality 5 within all sliding windows of 5 bp were mapped to the genome of strain N. gonorrhoeae MS11 (reference genome ASM15685v2). Annotation of non-coding RNAs was according to Remmele et al.(2014). Read mapping was conducted using Bowtie2 v2.1.0. DeSEQ2 version 1.6.2 was used to identify differentially regulated transcripts. Results: N. gonorrhoeae genes were identified which were upregulated or downregulated upon induced expression of sRNAs NgncR_237, NgncR_162 and NgncR_163. Conclusions: sRNA NgncR_237, NgncR_162 and NgncR_163 are involved in the regulation of genes involved in type IV pilus biogenesis, energy metabolism and transport processes.
2021-07-28 | GSE177032 | GEO
Project description:Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant and a complemented derivative were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, mRNA half-lives increased for 12 genes in Fe-depleted growth conditions, compared to FA1090. Biological functions for the 12 genes controlled by NrrF included energy metabolism, oxidative stress, antibiotic resistance, amino acid synthesis and a regulatory protein whose functions are not fully understood, in addition to hypothetical proteins. 18 samples. Three separate biological replicates for both growth conditions (Fe deplete and Fe replete) were done for all each isolate (6 samples per isolate); FA1090 wild type strain; NrrF_mutant strain LJ001; NrrF_complemented strain LJ002
2013-09-27 | E-GEOD-48526 | biostudies-arrayexpress